Compositions and methods for detecting markers associated with bladder cancer

Abstract

Compositions and methods for detecting bladder cancer are provided. In some embodiments, methods of monitoring recurrence of bladder cancer are provided. In some embodiments, the methods comprise detecting a set of markers consisting of CRH, IGF2, KRT20, and ANXA10.

What is claimed is: 
     
       1. A composition comprising a set of primers and a set of probes, wherein;
 a) the set of primers consists of
 i. a first and second primer for detecting CRH, 
 ii. a first and second primer for detecting IGF2, 
 iii. a first and second primer for detecting KRT20, and 
 iv. a first and second primer for detecting ANXA10; 
 
 b) the set of probes consists of
 i. a first probe for detecting a CRH amplicon, 
 ii. a second probe for detecting an IGF2 amplicon, 
 iii. a third probe for detecting a KRT20 amplicon, and 
 iv. a fourth probe for detecting an ANXA10 amplicon, wherein at least one primer or at least one probe is detectably labeled. 
 
 
     
     
       2. The composition of  claim 1 , wherein each said first and second primer produces an amplicon that is 50 to 500 nucleotides long, 50 to 400 nucleotides long, 50 to 300 nucleotides long, 50 to 200 nucleotides long, or 50 to 150 nucleotides long. 
     
     
       3. The composition of  claim 1 , wherein at least one said first and second primer spans an intron in the genomic sequence. 
     
     
       4. The composition of  claim 1 , wherein each said first and second primer spans an intron in the genomic sequence. 
     
     
       5. The composition of  claim 1 , wherein the first and second primer for detecting CRH comprise:
 a) a first primer comprising at least 12 nucleotides of SEQ ID NO: 19 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 20, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long; or 
 b) a first primer comprising at least 12 nucleotides of SEQ ID NO: 35 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 36, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long. 
 
     
     
       6. The composition of  claim 1 , wherein the first and second primer for detecting IGF2 comprise:
 a) a first primer comprising at least 12 nucleotides of SEQ ID NO: 16 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 17, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long; or 
 b) a first primer comprising at least 12 nucleotides of SEQ ID NO: 32 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 33, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long. 
 
     
     
       7. The composition of  claim 1 , wherein the first and second primer for detecting KRT20 comprise:
 a) a first primer comprising at least 12 nucleotides of SEQ ID NO: 13 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 14, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long; or 
 b) a first primer comprising at least 12 nucleotides of SEQ ID NO: 29 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 30, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long. 
 
     
     
       8. The composition of  claim 1 , wherein the first and second primer for detecting ANXA1O comprise:
 a) a first primer comprising at least 12 nucleotides of SEQ ID NO: 26 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 27, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long; or 
 b) a first primer comprising at least 12 nucleotides of SEQ ID NO: 38 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 39, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long; or 
 c) a first primer comprising at least 12 nucleotides of SEQ ID NO: 48 and a second primer comprising at least 12 nucleotides of SEQ ID NO: 39, wherein each primer is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long. 
 
     
     
       9. The composition of  claim 1 , wherein the first probe comprises at least 12 nucleotides of SEQ ID NO: 21 or at least 12 nucleotides of SEQ ID NO: 37, wherein the first probe is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long. 
     
     
       10. The composition of  claim 1 , wherein the second probe comprises at least 12 nucleotides of SEQ ID NO: 34 or at least 12 nucleotides of SEQ ID NO: 18, wherein the second probe is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long. 
     
     
       11. The composition of  claim 1 , wherein the third probe comprises at least 12 nucleotides of SEQ ID NO: 15 or at least 12 nucleotides of SEQ ID NO: 31, wherein the third probe is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long. 
     
     
       12. The composition of  claim 1 , wherein the fourth probe comprises at least 12 nucleotides of SEQ ID NO: 28 or at least 12 nucleotides of SEQ ID NO: 40, wherein the fourth probe is less than 50, less than 45, less than 40, less than 35, or less than 30 nucleotides long. 
     
     
       13. The composition of  claim 1 , wherein the composition is a lyophilized composition. 
     
     
       14. The composition of  claim 1 , wherein the composition is a solution. 
     
     
       15. The composition of  claim 14 , wherein the composition further comprises urothelial cells, or lysed urothelial cells. 
     
     
       16. The composition of  claim 1 , wherein at least one primer is detectably labeled, wherein the detectable label is a moiety selected from: a fluorescent moiety, a fluorescent energy transfer dye, a chemiluminescent moiety, a radiolabeled moiety, an electron spin label, and biotin. 
     
     
       17. A kit comprising the composition of  claim 1 , further comprising a first and second primer for detecting an endogenous control and/or a first and second primer for detecting an exogenous control. 
     
     
       18. The kit of  claim 17 , further comprising an endogenous control probe and/or an exogenous control probe. 
     
     
       19. The composition of  claim 1 , wherein at least one probe is detectably labeled, wherein the detectable label is a moiety selected from: a fluorescent moiety, a fluorescent energy transfer dye, a chemiluminescent moiety, a radiolabeled moiety, an electron spin label, and biotin.